Cell-based clustering using pixel clusters: Gaussian blur sigma=2, k=20, bin=0.5

Heatmaps of pixel clusters x markers

Compare pixel clusering with cell clustering

Cell-based FlowSOM clustering using all pixel clusters

No transformation

Normalize by total (covert from count to frequency), arcsinh transform, 99.99% normalization

Drop pixel clusters that do not have at least one marker ranked in top 5, normalize by total, arcsinh, 99.99% normalization

## [1] "Number of dropped clusters: 63"

## [1] "Dropped clusters: 1,2,3,4,5,6,8,9,10,11,12,13,14,15,18,19,20,23,24,25,26,27,28,30,31,33,36,37,40,41,42,43,46,47,48,49,50,51,52,55,58,60,61,62,68,69,71,76,77,78,79,80,81,82,83,84,85,86,87,89,90,93,94"

Cell-based FlowSOM clustering using pixel hierarchical clusters

No transformation

Normalize by total (covert from count to frequency), arcsinh transform, 99.99% normalization

Drop pixel clusters that do not have at least one marker ranked in top 2, normalize by total, arcsinh, 99.99% normalization

## [1] "Number of dropped clusters: 5"

## [1] "Dropped clusters: 3,5,6,7,15"